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Linux is a family of open source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991 by Linus Torvalds. Linux is typically packaged in a Linux distribution (or distro for short).
Distributions include the Linux kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name GNU/Linux to emphasize the importance of GNU software, causing some controversy.
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Unless you have a reason for the flatpak, just use the deb from the repo.
You cannot run flatpak application by simply calling the binary.
Coming to your question, I suggest you to install ffmpeg directly from your Debian repo, this way you can get hardware acceleration or device specific benefits for encoding/decoding/transcoding.
You can keep the flatpak version if it is needed by some other flatpak applications. Normally one won't interfere with the other.
Other parts of your system very likely require the apt ffmpeg. Keep it, or at least note the packages that apt wants to uninstall because they depend on ffmpeg